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You will typically find here notes and commentaries on the current biological literature. They are intended to document the post-reductionist, post-Darwinian revolution now in the making. The focus at present is on molecular biology — especially gene regulation and genomic studies as they bear on our understanding of organisms and their evolution. But the contextual, interlinked nature of everything going on in the organism means that you can expect occasional wide-ranging excursions in these commentaries.
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|Posted: May 15 2018||article 33|
The celebrated physicist Richard Feynman, skeptical of religious or mythic creation stories that focus upon humans and the meaning of their lives, once explained his doubt with arresting simplicity: “The stage is too big for the drama”.
It was a wonderfully succinct way to make his point, and suggests that Feynman had a bit of the poet in him.
The improbably large stage, which he found unsuited to our parochial origin myths, is, of course, the boundless frontier explored by cosmologists, whose probing, high-tech sensors have mapped inter-galactic dimensions of space and time so far beyond our immediate experience that we humans can scarcely hope to comprehend them.
We have all heard many times about our own nondescript place upon this vast stage. We are situated in an unremarkable galaxy among billions of others. Our solar system occupies a scarcely noticeable patch of real estate well out into this galaxy’s hinterlands. And, following the Copernican revolution, we earthlings lost even the circling attention of our neighboring sun and planets.
Still, we reigned unchallenged on our own planet, where we imagined ourselves the possessors of a special destiny, above all other creatures. But then, as a final insult, Darwin re-told our local creation story as a wearyingly long series of accidents, after which we found ourselves to be “trousered apes”.
Oh, the ignominy of it! Or, at least, that seems the usual point of the story. And, to be sure, it stings. The entire account can feel like a soul-crushing blow, rendering coarse or absurd all our higher aspirations, our ideals, our loves. . . .
|Posted: December 2017||article 32|
Not long ago an intelligent design advocate responded to one of my occasional swipes at ID theory. Thinking I had misinterpreted the theory, he said it was wrong to imagine the Designer working only in the remote past. “ID is open as to when the Designer implements Design”.
My response was along these lines:
For me, the issue isn’t whether a designer acted millions of years ago or a millionth of a second ago. Rather, it’s that the picture being offered is one of a designer working from outside upon a mechanical artifact. But organisms are not machine-like. Their activity is not an outcome of parts assembled by a designing engineer. They are not contrivances periodically requiring service by an outside agent for the sake of evolutionary progress. No, their very life consists of the activity through which they grow and transform their own physical means of acting.
Given today’s charged environment, you might wonder why I did not accuse my correspondent of being a “science-denier.” There is good reason. The label is a dastardly one, poisoning the spirit of evidence-based conversation, which is so crucial to science. It strongly suggests an inquisitorial demand for creedal belief rather than understanding. It almost inspires sympathy for intelligent design theory — and does inspire it for a number of the theory’s proponents, who can be fully as qualified as their authoritarian persecutors, and sometimes far more critically alert.
Some of those who labor to guarantee the purity of evolutionary orthodoxy habitually refer to intelligent design theorists as “IDiots” — and their argumentation naturally tends toward the same exalted level of discourse. To the shame of science, relatively few biologists have yet been willing to call out such behavior. It has mostly been outsiders who have urged greater scientific integrity. For example, the widely respected New York University philosopher, Thomas Nagel, has labeled the biological community’s treatment of intelligent design proponents “manifestly unfair” — this at considerable risk to his own reputation.
History teaches us that the kind of knee-jerk nastiness and vitriol leveled at ID theorists is not uncommon among competing sects trying to differentiate themselves from each other on fine points of sectarian doctrine — nuances that can assume gigantic importance in the minds of the disputants. You have to fight hardest with those who try to occupy your own ground.
That mainstream biologists are quarreling with ID theorists over common ground may seem a strange idea. But look again at the quoted paragraph above. As we will see more clearly in what follows, it applies without reservation to conventional evolutionary theory as well as ID. Few biologists are reticent about their conviction that organisms are machine-like and have been “tinkered” with throughout evolutionary history by a designer capable of producing intelligent results — all without any intelligent aid from organisms themselves.
The designer they have in mind, of course, is natural selection, which has famously been likened to a blind watchmaker and is almost universally referred to as an agent capable of intelligent activity. Selection shapes the bodies and behaviors of organisms, builds specific features, targets or acts on particular genomic regions, favors or disfavors (or punishes) various traits or behavioral strategies, operates in this way or that, maintains DNA sequences, promotes adaptation of populations to local environments, polices mutations and, in general, causes an endless variety of effects.
Not many biologists, whether ID proponents or otherwise, seem particularly interested in confronting the reality of intelligent agency where we observe it directly — in living beings — as opposed to taking the organism merely as evidence for the real guiding intelligence of their preferred Designer. This indifference toward organisms follows rather naturally when you have conceived them as machines, which always require an external designer. But we will take the alternative path, turning toward the organism’s inherent life.
|Posted: Mar 31, 2017||article 31|
When your dog takes a stick in its mouth, drops it at your feet, and then looks expectantly at you while signaling eagerness to run and retrieve the thrown plaything, you have no difficulty recognizing its intentions. Its behavior is blatantly purposive, even if its “state of mind” — whatever that might mean — is very different from yours and mine.
Similarly, if your cat is “telling” you it wants to go outdoors (cats, unfortunately, are always on the wrong side of the door), or if you have watched a bird building a nest, or an amoeba engulfing a particle of food, or the fish in a still pool darting toward the shelter of an overhanging bank upon your approach — you no doubt accept what you see without great puzzlement. We do not expect such behaviors from rocks, clouds, or volcanoes, but they seem normal for living things.
And so they are. Even the “growth behaviors” of plants and the “chemical behaviors” of the individual cells in our bodies are in some sense intelligent and purposive, wisely directed toward need-fulfilling ends. Purposive — or teleological (end-directed) — activity is no merely adventitious feature of living things. Being “endowed with a purpose or project”, wrote one of the twentieth century’s most influential biochemists, Jacques Monod, is “essential to the very definition of living beings”. And according to Theodosius Dobzhansky, a geneticist and leading architect of the past century’s dominant evolutionary theory, “It would make no sense to talk of the purposiveness or adaptation of stars, mountains, or the laws of physics”, but “adaptedness of living beings is too obvious to be overlooked ... Living beings have an internal, or natural, teleology”.
The curious thing, however, is that despite this emphatic recognition of the purposive organism, we find in textbooks of biology virtually no mention of purpose — or of the meaning and value presupposed by purpose. To refer to such “unbiological” realities is, it seems, to stumble into the unsavory company of mystics. Yet we might want to ask: if purposiveness in the life of organisms is as obvious as many in addition to Monod and Dobzhansky have admitted, why should it be impermissible for working biologists to reckon seriously with what everyone seems to know?
It’s a question we will ask. Be aware, however, that in struggling to answer it we may stir up unsettling doubts about the central biological concepts of evolution and natural selection.
|Posted: November 10, 2015||article 29|
Molecular biologists have spent several decades trying to identify how “one thing causing another” explains the organism. It is a simplistic and decontextualized way of looking that ends up in radical falsehood. The study of genes and their expression shows us that the organism is a living, intentional activity coordinating its parts in relation to the needs of the whole. Here I try to provide a glimpse of this whole at the molecular level. It is the fullest summary I can offer of how organisms employ their genes, and is preparation for a shift in my writing from gene regulation as such to a much more explicit consideration of the nature of organisms and their evolution.
|Posted: April 29, 2014||article 28|
In Part 1 and Part 2 of this series I have posed and approached the question: How can we understand our own highest conscious functions in relation to the wisdom we find throughout the living kingdoms? The latter includes everything from the intelligence of the chimpanzee and bacterium to the cells of our own bodies. Here in part 3 I try to offer what perspectives I can by way of an answer, while fully respecting the scientific modesty we must currently bring to the question. It’s a bit of a ride, and includes many highly readable (but brief) descriptions of some of the most amazing demonstrations of animal and plant wisdom you will ever hear about.
|Posted: March 26, 2015||article 27|
I suppose it’s finally become official: epigenetics is for real. Its certificate of reality has been issued by the Roadmap Epigenomics Consortium, which last month went public with a trove of reports in Nature and some of its sister publications. A news item on the Nature website summarized the import of the papers this way:
Almost every cell in the human body has the same DNA sequence. So why is a heart cell different from a brain cell? Cells use their DNA code in different ways, depending on their jobs — just as the orchestra [in an accompanying video presentation] can perform one piece of music in many different ways. The combination of changes in gene expression in a cell is called its epigenome.
The symphony orchestra metaphor has some promise. But, as we will see, it’s use in the Nature article is not particularly apt, if only because the “one piece of music” is not the supposed DNA code, but the organism as a whole.
But you say you’ve never quite figured out what epigenetics is? Well, you’re in excellent company. Many molecular biologists seem a little confused about it, too. But the confusion is also an opportunity, since clarifying epigenetics demands that we undo certain damaging intellectual habits within genetics and biology generally. This article is intended as a modest contribution toward that undoing.
|Posted: January 8, 2015||article 26|
In 2006 two Japanese researchers, S. Yamanaka and K. Takahashi, shook up the medical research world by announcing that they had “reprogrammed” adult mouse skin cells (in particular, fibroblasts) to become induced, pluripotent stem cells. Their method: add to the cultured adult cells just four well-chosen genes that result in the over-expression of four gene-regulatory proteins.
This was a time when the debate over the use of stem cells obtained from human embryos was fierce, so the idea that a stem cell might be created (“induced”) from a normal adult skin cell produced quite a sensation.
Laboratories the world over have been running with this discovery ever since, and there were already significant developments by the time I found myself giving a talk at a conference involving a number of molecular biologists. Not having familiarized myself with the work on induced pluripotency, I did not discuss it in my talk, but I did emphasize what seemed to me a decisively important point: there are no “central controllers” or “master regulators” in the cell.
During the discussion period afterward, a researcher at one of the nation’s major stem cell research laboratories aggressively challenged me by stating flatly: “You’re wrong. There are master regulators in the cell. We prove it every day in our laboratory, where we insert just three or four transcription factors in a differentiated cell and cause it to revert to a pluripotent stem cell”.
At the time I could only vaguely allude to research results that, as I was peripherally aware, were already coming in — and then add, “Wait and watch, and you will see. I have no doubt whatever that your master regulators are an illusion”.
|Posted: December 9, 2014||article 25|
A rapidly swelling literature is testifying to the dependence of human welfare upon the diverse microorganisms — collectively, the microbiome (or microbiota) — we play host to. By common admission, we have hardly begun to figure out how these microorganisms affect us — or, I should perhaps say, how they are part of us. But we know enough to appreciate that we could not live normally and healthily (if we could live at all) without them.
The bacteria and other microorganisms in our gut typically outnumber the cells in our body by a factor of ten to one, and their collective genome is orders of magnitude larger than our “own” genome. Remarkably, “one-third of the metabolites in the blood are coming from gut bacteria”, according to Phillip Hylemon, a microbiologist and immunologist at Virginia Commonwealth University in Richmond. Altogether, our microorganisms “function as another organ, complementing and interacting with human metabolism in ways not fully understood”.
You’ll have a hard time believing how the invisible microbes within us function as part of our own life. And perhaps not so hard a time believing how biologists are tempted immediately to regard particular microorganisms as opportunities for exerting neat control over everything from liver cancer to autism.
|Posted: November 11, 2014||article 24|
In biology, the problem of the morphological “type”, or characteristic form, raises the question, When can different features be declared in some sense “the same”? Are the fin of a whale, the wing of a bird, and the arm of a primate the same limb? And if so, what are we recognizing as the common identity? We can ask similar questions when we consider the succession of bones along the spine of a vertebrate, or the succession of leaves along the stem of a plant. In what sense, if any, can we regard these as transformations of a single form? And what might that single form be?
In this article I attempt to summarize an exploration of these questions by the late philosopher, Ronald Brady. Drawing particularly on Johann Wolfgang von Goethe’s work and focusing especially on a leaf sequence along the stem of a single buttercup, he is led to conclusions of dramatic importance. We cannot extract from the leaves a set of common features that enables us to define, in any biologically significant sense, how these leaves “hold together” as a single form. Nor can we find or invent a static schema that generalizes over all the individual leaves. What we actually discover is a unified transformational movement, or gesture, with the individual forms being “snapshots” derived from the gesture.
The transformational movement, as a single gesture, is revealed not only through the sameness of the individual forms in a developmental series, but also through their characteristic differences. A typical or archetypal movement of this sort must continually change in order to remain itself. Moreover — and however much this goes against current thinking — this movement must be regarded as causal in nature. It is the generative principle through which the individual buttercup leaves gain their “buttercup character”.
Brady’s treatment of form and causation contrasts sharply with both conventional biological thinking and the vitalist tendencies that so naturally infect this thinking. It also contrasts with any imputation to organisms of purpose and design analogized either to human purposes and designs or to mechanical operations.
|Posted: September 9, 2014||article 23|
Nine years ago Richard Conn Henry, an astrophysicist at Johns Hopkins University, published an opinion piece in Nature entitled “The Mental Universe”. He urged the scientific community to repeat Galileo’s achievement in “believing the unbelievable”, and recalled Sir James Jeans’ famous remark that “the Universe begins to look more like a great thought than like a great machine”. We don’t know all that this implies, he continued, “but — the great thing is — it is true. ... The Universe is immaterial — mental and spiritual. Live, and enjoy”.
The most dramatic thing about the article was the lack of drama: it produced no visible controversy. After all, physicists have long been accustomed to receive such assertions peaceably, because the science itself seems tolerant of them.
But suppose Henry had made a narrower and more modest claim — just a small part of what he implied in “The Mental Universe”. Suppose he had written only of “The Mental Cell”. Would the occasion have been equally unremarkable? Most molecular and cellular biologists, I suspect, will readily picture the unseemly consequences likely to follow upon the appearance of words like immaterial, mental, and spiritual in their published papers. It would be as if an unspoken taboo were violated.
|Posted: August 1, 2014||article 22|
Vladimir Solovyov (1853-1900) was a Russian philosopher, theologian, literary critic, and poet. His little book, The Meaning of Love — published in the early 1890s, long before the era of sociobiology — is as trenchant and relevant a counterpoint to that modern discipline as you are likely to find today.
I offer here a straightforward summary of parts of Solovyov’s argument, allowing it to stand on its own despite the limitations of nineteenth-century biological knowledge and despite expressions that are bound to grate on modern ears. Yes, the ideas presented here reflect Solovyov’s peculiar era and culture and may therefore appear oddly provincial and dated. But this can usefully remind us that our own thought-forms are, in at least some respects, equally provincial and dated — and will be experienced as such by others soon enough. Far better if we don’t leave that experience entirely to them. Sometimes the easiest way out of the unconsciously constraining assumptions of one’s own cultural context is to listen as earnestly and sympathetically as possible to the “alien” testimony of an earlier era or foreign culture.
These words by Owen Barfield in the book’s preface may serve as an Abstract:
[Solovyov] opens with a biological survey which easily, and to my mind irresistibly, refutes the age-old assumption ... that the teleology of sexual attraction is the preservation of the species by multiplication. On the contrary, it is apparent from the whole tendency of biological evolution that nature’s purpose or goal (or whatever continuity it is that the concept of evolution presupposes) has been the development of more complex and, with that, of more highly individualized and thus more perfect organisms. From the fish to the higher mammals quantity of offspring steadily decreases as subtlety of organic structure increases; reproduction is in inverse proportion to specific quality. On the other hand, the factor of sexual attraction in bringing about reproduction is in direct proportion. On the next or sociological level he has little difficulty in showing that the same is true of the factor of romantic passion in sexual attraction. Both history and literature show that it contributes nothing towards the production of either more or better offspring, and may often, as in the case of Romeo and Juliet, actually frustrate any such production at all.
Why then has nature, or the evolutionary process, taken the trouble to bring about this obtrusively conspicuous ingredient in the make-up of homo sapiens? . . .
Being, at the level of human individuality, is characterized above all by a relation between whole and part that is different from the everyday one that is familiar to us. We may catch a glimpse of it if we reflect, in some depth, on the true nature of a great work of art. ... It is a relation no longer limited by the manacles of space and time, so that interpenetration replaces aggregation; one where the part becomes more specifically and individually a part — and thus [to that extent] an end in itself — precisely as it comes more and more to contain and represent the Whole.
Sex-love is for most human beings their first, if not their only, concrete experience of the possibility of such an interpenetration with other parts, and thus potentially with the Whole.
|Posted: July 3, 2014||article 21|
Almost everything you read in the literature of molecular biology today testifies to the seemingly irresistible yet highly problematic search for clearly defined causes as the essential elements of biological understanding. But the more fundamental elements of understanding are contexts possessed of their own expressive character. Here we look at some typical research reports, each of which bears out this truth in its own way.
Viruses, cytoplasmic DNA, and the web of life
The (molecular) days of our lives
DNA and RNA brought to life
Functional vs. nonfunctional DNA binding
|Posted: June 10, 2014||article 20|
From humans to bacteria, every organism is a cognitive creature, carrying out mind-like functions in every aspect of its life. All biologists know this, even if they are strongly encouraged by the reigning intellectual climate to forget it. You can think of this article simply as my way of helping to keep the truth within sight.
It is essential, however, not to pre-judge the term “mind-like”, whose meaning should become clearer in the following text. Be aware that one might speak of the mind-like aspects of simpler organisms (1) without suggesting that these organisms have minds in anything like the familiar human sense, and (2) while recognizing that the effective wisdom playing through the simplest, one-celled organism far transcends any mental achievements we humans are consciously capable of.
|Posted: May 15, 2014||article 19|
A while back I published a criticism of intelligent design (ID) theory entitled “A Sectarian Quarrel? Intelligent Design and Neo-Darwinism”. This was followed more recently by a brief footnote on the same theme, which in turn led to a response on the “home page” of the ID movement — the Discovery Institute’s “Evolution News and Views” website.
Given the ongoing and seemingly intensifying “culture wars” involving (among others) conventional biologists, ID theorists, and a militant cadre of religiously anti-religious “new atheists”, it seems worthwhile to explore some of the issues while ignoring the usual sound and fury. I have addressed the following directly to the theorists of the ID movement, partly as a response to their response to my criticism, but more centrally as an effort of mutual understanding.
To keep the article at a reasonable length, I have had to assume the reader’s familiarity with the general contours of intelligent design theory. Unfortunately — as I have learned by immersing myself in a good deal of ID literature, both pro and con — the public in general has been one-sidedly subjected to the most shamefully (and often intentionally) distorted talking points on the subject, courtesy of what appears to be a very threatened biological establishment.
As for my own severe questioning of intelligent design offered here, I don’t believe you will find much like it anywhere on the current intellectual landscape.
|Posted: April 24, 2014||article 18|
When someone persistently hallucinates, seeing things that aren’t there, we usually assume a cognitive aberration of some sort, if not a severe mental illness. What, then, to make of those countless biologists who look at organisms and think they are seeing machines? Or who look at organs, cells, organelles, and even molecules, and see machines within machines?
I will leave it for you to judge. However, one thing is certain: an inexcusable mistake has gripped the scientific community for decades, severely perverting biological understanding.
I have previously tried to explain in various places why the analogy between organisms and machines fails utterly. But in reading the biological literature lately, I have found the insistent appeals to machinery so egregious, so viciously destructive of scientific insight, and so contrary to the obvious evidence, that I have myself been driven rather too close to a pathological reaction, or at least to an unhelpful exasperation. And so I have decided to gather my thoughts together in what I hope will be a more concise and effective statement.
A good place to start is with a concrete example. ...
|Posted: March 31, 2014||article 17|
Hox genes, often cited as “controllers” of organismal form, turn out to be dependent for their expression on the various factors that control their spatial form in the nucleus.
In a second paper, metabolism is proposed as a replacement for DNA at the head of important causal chains in the organism.
And a special issue of the journal Cell looks for the unifying threads that make sense of the tidal waves of isolated data available to biologists today. Where can those threads be found, if not in the whole organism, as a unity, and not in any particular parts?
In sum, as the feverish obsession with DNA as First Cause continues to lose its force, we may be seeing a long-delayed effort to understand the whole organism. (However, the language of researchers continues to reflect the search for “controlling” elements.)
|Posted: February 11, 2014||article 16|
A molecular web of life
Protein-coding RNAs (messenger RNAs) have been discovered in large communities of mutual regulation. The result of their intricate interplay is an adjustment of gene and protein expression so complex, so fluid, and so continually varying in its details as to blur the distinction between regulators and objects of regulation — and pose insuperable challenges for analysis.
From static to dynamic understanding
A key question is this: when vast numbers of molecules are participating in extended, highly articulated, and directional cellular processes such as cell division or RNA splicing, what keeps them “on-script” when there are a thousand other things they might do — and will do in different contexts? This question is underappreciated due to a lack of imagination in picturing what we already know about how every specific molecular process adapts to the fluid, ever-changing conditions within the organism.
Explaining from the whole to the part
If we are faithful to observation, we recognize that in the organism the larger pattern, or context, should, in the proper sense, be seen as the cause of the the part-processes through which the pattern comes to manifestation. This is the stumbling block for conventional scientists of a materialistic bent. Yet it turns out to be a truth that they implicitly accept and work with all the time.
Courage to name the unknown
Sometimes the prerequisite for scientific advance is courage to put a name to the clearly indicated borders of an unknown territory — a territory we know is there and to which we can assign a definite place in the larger scientific scheme of things, but whose nature and characteristic mode of functioning we do not yet understand. The forming agency so obviously at work in the organism is one such “nameable unknown”.
|Posted: January 16, 2014||article 15|
This article ranges widely in a way that will doubtless surprise you. Some random excerpts:
[Regarding the organization of cells in a hair follicle:] Dramatically, the authors show that “niche stem cells can be dispensable for tissue regeneration, provided that the overall integrity of the niche is maintained”. When the stem cell population in the bulge or hair germ is destroyed by laser ablation, distant epithelial cells flow toward the damaged compartment and go through a transformation of identity enabling them to replace the lost cells. As the authors summarize it, “The overall structure and function of the tissue is maintained because cells are capable of adopting new fates as dictated by their new niche microenvironment”.
It is impossible to reconcile these goings-on in the hair follicle with the picture of an organism being constructed from an available collection of well-defined parts as building blocks. The larger context helps to “decide” what sorts of elements it will have, how they should be transformed, and how they will come into mutual relationship. Nothing could be further from the common picture of the organism or the cell as a product of bottom-up causation, where the sole basis for understanding consists of putting back together in our minds the parts we have previously analyzed out of — and severed from — their life-receiving connection to the whole.
. . . .
When biologists speak of the organism’s activity, who exactly do they mean to say is performing that activity? When they acknowledge that something in the organism is context-dependent, what in fact is it dependent upon — what agency, or unified sphere of activity, or principle, or lawfulness, or other reality of any sort are they appealing to? They cannot be pointing merely to a particular collection of objects, because the collection can be endlessly varied or perturbed, and yet the context remains more or less coherent, and the organism more or less maintains its character. What is coherent? What has this character?
. . . .
I have been emphasizing that the organism is a becoming. This fact makes a lie of the overly emphatic conviction that we learn who we are through a study of evolution. Evolution tells us a great deal — but only about our past. It doesn’t tell us about the potentials of our becoming in the present. When we learn that such-and-such a trait of lower animals is recognizable in ourselves in some form, this knowledge immediately changes our relation to that trait. It opens up a space of freedom to do work and act consciously where previously, rather as with those monarch butterflies migrating south, nature was simply acting through us. “The truth will make you free”. Those who delight in pointing out our “lower nature” are actually assisting us — presumably to their great disappointment, should they become aware of it — toward the realization of a higher nature.
|Posted: December 5, 2013||article 14|
Organisms do things; rocks have things done to them. Even at rest a cat is doing something; rocks do not rest, but are brought to rest. An organism is always engaged in tasks, always going somewhere. Its activity is directed and in some sense intentional and purposeful (“teleological”). Its judgments in responding appropriately to environmental challenges reflect a profound biological wisdom.
From the molecular level on up, organisms mobilize their resources in order to achieve things, whether replicating DNA, splicing RNA, orchestrating cell division, forming embryonic organs, healing wounds, breathing, constructing a nest, securing food, caring for offspring, shedding a skin, maintaining body temperature, hibernating, or anything else we can properly regard as biological activity. Such activity is always part of a life story, and the protagonist in that story is in some sense what every story protagonist must be: a reasoning agent.
This reasoning agent is one of the many wildly diverse creatures on earth whose appearance and ways may strain our credulity and challenge our imagination. Yet, however bizarre its metamorphosing appearance and life cycle may appear to us, its complex and fine-tuned qualitative intelligence is unerring, enabling it to hold itself together and “stay in character” throughout its life and development, even as it differentiates itself internally into a community of organs and tissues that may be as wildly diverse as any external ecological community.
But you will already have asked, quite rightly, what is meant by “reasoning agent”? And even if we are driven to use such a phrase, how can we distinguish an aphid’s “reasoning” from that of a nuclear physicist? This is the question I will address here. Until we sort the matter out, the language of the preceding paragraphs (and of the paragraphs immediately following — and even much of the standard biological literature) invites horrible misunderstandings. Note that I have already twice said, in some sense. We must be on our guard.
|Posted: November 14, 2013||article 13|
It’s become increasingly clear in recent years, that, quite apart from its organelles and cytoskeleton, the cytoplasm is elaborately and “invisibly” organized. Various macromolecular complexes, in more or less defined mixes, congregate in specific locations and sustain a collective identity, despite being unbounded by any sort of membrane. Here we’re looking at structure without even a pretense of mechanically rigid form. How do cells manage that?
A couple of years ago a research duo from the Max Planck Institute of Molecular Cell Biology and Genetics in Dresden, and the Department of Chemical and Biological Engineering at Princeton University, writing for the journal, Developmental Cell, framed the problem this way:
“Non-membrane-bound macromolecular assemblies found throughout the cytoplasm [inner contents of the cell] and nucleoplasm [contents of the nucleus] ... consist of large numbers of interacting macromolecular complexes and act as reaction centers or storage compartments. ... We have little idea how these compartments are organized. What are the rules that ensure that defined sets of proteins cluster in the same place in the cytoplasm? (Hyman and Brangwynne 2011)
Even more puzzling, a “compartment” can maintain its identity despite the rapid exchange of its contents with the surrounding cytoplasm. “Fast turnover rates of complexes in compartments can be found throughout the cell. How do these remain as coherent structures of defined size and shape when their components completely turn over so quickly?”
[Read More (Note: the above excerpt is not at the article’s beginning).]
|Posted: October 24, 2013||article 12|
This article is a brief introduction and commentary relating to a new paper appearing on the “Biology Worthy of Life” website: “Look What’s Happened to Genetic Synonyms!”
Following immediately upon the discovery of the double helical structure of DNA in 1953, some of the most brilliant scientists from several disciplines pooled their efforts in a feverish quest to lay bare the secret of the “genetic code”. Their invigorating struggle lasted about a decade, and ever since then, the code has lain at the foundation of biological understanding — and misunderstanding.
The aim of the decoding effort was to learn how the “letters” of a DNA sequence mapped to the amino acid sequence of the cognate protein. As it turned out, the solution was rather disappointing, as most scientists saw it. Having anticipated the most elegant bit of computer-like programming imaginable, they found a genetic code they could only term “redundant” or “degenerate” because of its apparent inefficiency. It was as if the dots and dashes of the Morse code mapped to the English alphabet, not one-to-one, but rather with individual English letters corresponding to several different dot-dash patterns.
|Posted: September 29, 2013||article 11|
One of the unquestioned certainties of the human genome has long been that nearly all cells in our bodies contain identical DNA. (Some cancerous tissues and certain immune cells are major known exceptions.) Another truth has seemed so evident as to require little explicit statement: DNA knows its proper place in the cell, and stays there. Yet on both counts the reigning convictions have turned out to be more than a little shaky. And on both counts the emerging evidence testifies to yet more things the organism does to manage its own genome.
In a previous posting I reported on our “genetically mosaic” bodies, describing how different groups of cells or tissues in the same body possess somewhat different genomes. This, of course, contravenes a long-running assumption about the overall genetic uniformity of the organism. There was supposed to be just one “plan” (or “recipe” or “Book of Life”), not many variants of it. If there are different versions of the plan, then either biologists will be sent on a fruitless search for a distinct “master plan” that “controls” the relations between the subordinate plans, or (one rather hopes) they will begin to give more credence to the agency of the organism itself as a living whole — the organism they already incessantly speak of as a thoughtful agent.
Here I will add something about the refusal of DNA to stay where it “belongs”. Indeed, the remarkable thing is that DNA, so often viewed as an endpoint of cell signaling, has now been found to look suspiciously like a signaling molecule itself. Or, at least, fragments of it do. ...
|Posted: September 12, 2013||article 10|
I’ve just finished reading Darwin’s Doubt, a newly released critique of mainstream (neo-Darwinian) evolutionary theory and a defense of intelligent design. The author is Stephen Meyer of Seattle’s Discovery Institute, an organization often considered to be the chief incubator of the intelligent design movement.
Here I offer no summary or review of the book, but only a single and (so I believe) decisive line of thought. I should say first, however, that, as an assessment of the challenges facing evolutionary theorists on several fronts today, the book seems to me at least as creditable as many productions by contemporary neo-Darwinian biologists. And, in his attempt to convince the reader through calm argument, the author rises above the shrill, apparently frightened, and scarcely scientific rhetoric we’ve been hearing for years from some of the more militant, self-identified atheists and anti-intelligent design types.
As most long-time readers will have recognized, I am no more an intelligent design type myself than I am a conventional Darwinian thinker. And in fact my aim now is to characterize the common ground upon which those two camps have taken up arms, and to suggest that they might achieve a healthy détente by simply abandoning their unproductive field of battle and turning toward the organism itself. ...
|Posted: August 22, 2013||article 9|
In 1992 the preeminent geneticist, Walter Gilbert, memorably dramatized the significance of the Human Genome Project by telling audiences how in the future every individual’s genomic sequence will be inscribed on a digital disk. He then illustrated this future by pulling a CD out of his pocket, holding it up, and saying, “Here is a human being; it’s me”.
It now appears likely, however, that when such a future comes he will need to carry around many disks, each containing a unique digital sequence corresponding to one of the multiple genomes in his own body. His problem will then be to decide which disk holds the real Walter Gilbert. ...
|Posted: August 2, 2013||article 8|
A dose of ionizing radiation equal to 10 grays (a measure of absorbed radiation) is lethal to the human body. Most bacteria cannot survive 200 grays. But then there is the bacterium known as Deinococcus radiodurans: it can endure over 17,000 grays and do quite well, thank you. Never mind that its genome is thoroughly shattered by the assault.
Here’s what happens. Ionizing radiation can damage DNA in various ways, perhaps worst of all by causing double-strand breaks. These are breaks across both strands of the DNA double helix. The familiar bacterium, E. coli, not at all untypically, dies when it suffers about four double-strand breaks per each of its four-to-eight circular DNA molecules. Deinococcus radiodurans, by contrast, can survive over a thousand double-strand breaks. This means that it continues life after its genome is broken into hundreds of small fragments. It does so by proceeding to put its genome back together again when living conditions improve — a daunting task, to say the least. ...
|Posted: July 19, 2013||article 7|
On the Biology Worthy of Life website I have posted a new document entitled, “How the Organism Decides What to Make of Its Genes". It is perhaps the strangest piece I have ever published, being the only one I would advise you not to try to read. It is also the only one almost guaranteed in advance to contain at least some bits of misleading information. And, most importantly, it may be the one most likely to seriously mess with the heads of practicing biologists, many of whom (I have slowly come to recognize) are so burdened by the demands of their narrow fields of research that they may scarcely be aware of much of the literature even in disciplines rather closely related to their own. The document in question is intended to provide the kind of healthy shock that may come from suddenly gaining a much wider vantage point. ...
Pervasive Transcription: Using Genomes “Every Which Way” (article 6, July 4, 2013)
Are “Disordered” Proteins Really Disordered? (article 5, June 25, 2013)
What Absent Genes Don’t Do — And How Can We Know? (article 4, June 15, 2013)
The Paradox in “Explaining” Form (article 3, June 15, 2013)
The Complex Performance of the Three-Dimensional Chromosome (article 2, June 10, 2013)
Signals and the Whole Organism (article 1, June 7, 2013)
This document: RediscoveringLife.org
Steve Talbott :: Rediscovering Life